GSV: a web-based genome synteny viewer for customized data

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Article discussing the genome synteny viewer (GSV), a web-based viewer providing a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser.

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4 p.

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Revanna, Kashi V.; Chiu, Chi-Chen; Bierschank, Ezekiel & Dong, Qunfeng 2011.

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This article is part of the collection entitled: UNT Scholarly Works and was provided by UNT College of Arts and Sciences to Digital Library, a digital repository hosted by the UNT Libraries. It has been viewed 139 times . More information about this article can be viewed below.

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Article discussing the genome synteny viewer (GSV), a web-based viewer providing a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser.

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4 p.

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Abstract: Background: The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis. Results: The authors have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation. Conclusions: GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas.bioinfo.cas.unt.edu/gsv, and the software is also freely available for local installations.

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  • BMC Informatics, 2011, London: BioMed Central Ltd.

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  • Publication Title: BMC Bioinformatics
  • Volume: 12
  • Issue: 316
  • Peer Reviewed: Yes

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UNT Scholarly Works

The Scholarly Works Collection is home to materials from the University of North Texas community's research, creative, and scholarly activities and serves as UNT's Open Access Repository. It brings together articles, papers, artwork, music, research data, reports, presentations, and other scholarly and creative products representing the expertise in our university community.** Access to some items in this collection may be restricted.**

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  • 2011

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  • March 2, 2012, 11:47 a.m.

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  • May 14, 2014, 12:47 p.m.

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Revanna, Kashi V.; Chiu, Chi-Chen; Bierschank, Ezekiel & Dong, Qunfeng. GSV: a web-based genome synteny viewer for customized data, article, 2011; [London, United Kingdom]. (digital.library.unt.edu/ark:/67531/metadc77111/: accessed January 23, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Arts and Sciences.